You are basically saying that whatever someone believes is fine as long as they really believe it is true. Muslims believing they got a command from Hashem is NOT the same as Bnei Yisrael actually getting a command from Hashem. Judaism and Islam are not comparable. They are not two religions. Judaism is the truth, Islam is a man-made religion and perversion of the truth.We are responsible for and judged for what we believe. The Muslims will be judged for believing in a prophet that doesn’t take much to disprove. They will be held responsible and they will be judged for killing in the name of that prophet.
(As an aside, Hashem gave us an inborn sense of morality for a reason. It’s supposed to lead us to the recognition of the truth.)
In general we are not allowed to kill etc. However if Hashem tells us to, we must – and if I remember correctly, the people fighting were given a promise that if they are doing so only because Hashem said so, it will not numb their midah of rachmanus.)